TY - JOUR
T1 - Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system
AU - Shin, Dong Guk
AU - Lee, Changhwan
AU - Zhang, Jinghui
AU - Rudd, Kenneth E.
AU - Berg, Claire M.
N1 - Funding Information:
We would like to thank Webb Miller for providing us with PrbMkr C source code prior to publication and Fred Maryanski for making the ONTOS system available for our implementation. We also thank T.C.Ting. Steve Demurjian and Joe Leone for numerous discussions about C + + and object-oriented concepts, and Robert Robbins for his encouragement in this endeavor. This work was supported by National Science Foundation grant DIR-9019069. Department of Energy grant DE-FG02-89ER-60862 and the University of Connecticut Research Foundation.
Copyright:
Copyright 2010 Elsevier B.V., All rights reserved.
PY - 1992/6
Y1 - 1992/6
N2 - This paper reports our exploratory work to redesign, implement and integrate a collection of genome software tools with an object-oriented database system. Our software tools deal with genome data from Escherichia coli K-12, a bacterium that has been studied intensively and provides richer data sets than any other living organism. The object-oriented DBMS used for the integration is ONTOS, a commercial object-oriented system from Ontologic Inc. This redesign and implementation task was performed in two steps. First, C programs were converted into C++, and then the C++ version programs were modified and integrated with an object-oriented modeling of the data to form an ONTOS database application. The first step helps us develop a conceptual view for a DBMS-independent object-oriented construct. The second step elucidates what additional DBMS-dependent modification steps are needed to provide persistency to the objects. Examples are included to illustrate steps of the redesign and implementation. Overall, the outcome of this project demonstrates that programs and data can be successfully integrated with an object-oriented database, while providing the objects with persistency and shareability. This paper includes discussions using concrete examples on what advantage the object-oriented database approach provides over the relational database approach.
AB - This paper reports our exploratory work to redesign, implement and integrate a collection of genome software tools with an object-oriented database system. Our software tools deal with genome data from Escherichia coli K-12, a bacterium that has been studied intensively and provides richer data sets than any other living organism. The object-oriented DBMS used for the integration is ONTOS, a commercial object-oriented system from Ontologic Inc. This redesign and implementation task was performed in two steps. First, C programs were converted into C++, and then the C++ version programs were modified and integrated with an object-oriented modeling of the data to form an ONTOS database application. The first step helps us develop a conceptual view for a DBMS-independent object-oriented construct. The second step elucidates what additional DBMS-dependent modification steps are needed to provide persistency to the objects. Examples are included to illustrate steps of the redesign and implementation. Overall, the outcome of this project demonstrates that programs and data can be successfully integrated with an object-oriented database, while providing the objects with persistency and shareability. This paper includes discussions using concrete examples on what advantage the object-oriented database approach provides over the relational database approach.
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U2 - 10.1093/bioinformatics/8.3.227
DO - 10.1093/bioinformatics/8.3.227
M3 - Article
C2 - 1633564
AN - SCOPUS:0026628613
VL - 8
SP - 227
EP - 238
JO - Bioinformatics (Oxford, England)
JF - Bioinformatics (Oxford, England)
SN - 1367-4803
IS - 3
ER -